Many people seem to feel the same way, but I still don't understand why. The only part of it that really irritates me is how few programs allow you to pin the size of the subwindow to the main window so that they remain related, but I suppose that could be enough.
What's funny about it is that it actually came from providing a superior alternative to other desktop operating systems, most of which did the same thing originally. e.g. on the early MacOS, you had only fullscreen applications with subwindows, and only Desk Accessories could float over them. On AmigaOS, each application had its own "screen" which could be raised or lowered, and you could pull them up or down the screen, so you could show the top of one screen over the bottom of another. Each AmigaOS screen could have its own palette, which was special; MacOS couldn't do that. Windows' MDI couldn't do it either, but you could at least treat those applications the same way you would treat any other window. But once we got 24 bit color, all that stuff was outdated, and everybody else was letting you just mix windows freely.